[phenixbb] More problems with HEM.cif?

Yarrow Madrona amadrona at uci.edu
Thu Jun 19 17:02:28 PDT 2014


Yea,
That was dumb. Sorry. Vinyl is a double bond. Sleepy time for me.



On Thu, Jun 19, 2014 at 1:32 PM, Edward A. Berry <BerryE at upstate.edu> wrote:

> No, those are actually double bonds (hence the name "vinyl"),
> unless it it is a c-type heme, in which case you should be using HEC.cif
> $CCP4/lib/data/monomers/h/HEM.cif:
>  HEM      CBC    CAC       double      1.329    0.020
>  HEM      CBB    CAB       double      1.330    0.020
> $CCP4/lib/data/monomers/h/HEC.cif
>  HEC      CBC    CAC       single      1.510    0.020
>  HEC      CBB    CAB       single      1.510    0.020
> This is because cysteine Sg's covalently link the vinyl groups,
> adding across the double bond as it were.
> Unless you have trypanosome or Euglena cytochrome,
> in which case one vinyl is native and the other
> is substituted by cysteine.
> eab
>
>
> On 06/19/2014 03:11 PM, Yarrow Madrona wrote:
>
>> Hello,
>>
>> The HEM.cif in  $Phenix/chem_data/mon_lib
>> has ideal angles of 1.337 for single bonds on the vinyl groups.
>>
>> HEM   CAC     CBC   coval         1.337 0.02
>>
>> HEM   CAB     CBB   coval         1.337 0.02
>>
>> As far as I know these are single bonds and the ideal bond angles should
>> be around 1.5.
>>
>> -Yarrow
>>
>>
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>>
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